Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie.

IF 3.3 3区生物学

Genetics Pub Date : 2021-07-14 DOI:10.1093/genetics/iyab074

Ales Varabyou, Christopher Pockrandt, Steven L Salzberg, Mihaela Pertea

引用次数: 0

Abstract

The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies. However, in case of the SARS-CoV-2, the low divergence of near-identical genomes sequenced over a short period of time makes conventional analysis infeasible. Using a novel method, we identified 225 anomalous SARS-CoV-2 genomes of likely recombinant origins out of the first 87,695 genomes to be released, several of which have persisted in the population. Bolotie is specifically designed to perform a rapid search for inter-clade recombination events over extremely large datasets, facilitating analysis of novel isolates in seconds. In cases where raw sequencing data were available, we were able to rule out the possibility that these samples represented co-infections by analyzing the underlying sequence reads. The Bolotie software and other data from our study are available at https://github.com/salzberg-lab/bolotie.

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利用 Bolotie 快速检测 SARS-CoV-2 中的支系间重组。

检测病原体基因组重组的能力对于系统发育分析的准确性至关重要，因此也是预测传染病传播、制定治疗方法和公共卫生政策的关键。然而，就 SARS-CoV-2 而言，短时间内测序出的近乎相同的基因组差异较小，使得传统分析变得不可行。我们采用一种新方法，在首批发布的 87,695 个基因组中发现了 225 个可能来自重组的异常 SARS-CoV-2 基因组，其中几个基因组在人群中持续存在。Bolotie 专为在超大数据集上快速搜索支系间重组事件而设计，有助于在数秒内分析新型分离株。在有原始测序数据的情况下，我们能够通过分析基础序列读数来排除这些样本代表合并感染的可能性。Bolotie软件和其他研究数据可在https://github.com/salzberg-lab/bolotie。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genetics 生物-遗传学

CiteScore

6.20

自引率

6.10%

发文量

177

期刊介绍： GENETICS is published by the Genetics Society of America, a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work. While it has an illustrious history, GENETICS has changed along with the communities it serves: it is not your mentor''s journal. The editors make decisions quickly – in around 30 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is a peer reviewed, peer-edited journal, with an international reach and increasing visibility and impact. All editorial decisions are made through collaboration of at least two editors who are practicing scientists. GENETICS is constantly innovating: expanded types of content include Reviews, Commentary (current issues of interest to geneticists), Perspectives (historical), Primers (to introduce primary literature into the classroom), Toolbox Reviews, plus YeastBook, FlyBook, and WormBook (coming spring 2016). For particularly time-sensitive results, we publish Communications. As part of our mission to serve our communities, we''ve published thematic collections, including Genomic Selection, Multiparental Populations, Mouse Collaborative Cross, and the Genetics of Sex.